Over and over, I’d install the latest Lunchbox (For Dynamo 1.0 on Revit 2016)…
it would work until the next Revit restart, then it would be gone:
Workaround
Set the folder to read only…
and it seems to stick around.
I’ve been having the same problem. This fixes it but makes updates to packages a real pain. 
Wish I knew what was causing it…
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Wondering if this issue reported on GitHub and if the developer team have done anything about it?
I’m having the same issue on Dynamo 1.3
I’ve seen issues where a similar package was saved on two locations and dynamo was trying to upload them both. I.E.: lunchbox package installed on both the local drive and the network drive, or multiple versions on the local drive.
Try opening any node in the package based off its location on your drive - if this fixes the issue you can use that as a workaround in the meantime.
Upload a screenshot of your package locations (I believe this is under Settings > manage node and package paths) if you’re not sure if that is the case.
One of the responses on this, or another, thread talked about an edit to a Dynamo config file. That change solved it for me.
Greg McDowell Jr